Causes of death identified in neonates enrolled through Child Health and Mortality Prevention Surveillance (CHAMPS), December 2016 –December 2021

Each year, 2.4 million children die within their first month of life. Child Health and Mortality Prevention Surveillance (CHAMPS) established in 7 countries aims to generate accurate data on why such deaths occur and inform prevention strategies. Neonatal deaths that occurred between December 2016 and December 2021 were investigated with MITS within 24–72 hours of death. Testing included blood, cerebrospinal fluid and lung cultures, multi-pathogen PCR on blood, CSF, nasopharyngeal swabs and lung tissue, and histopathology examination of lung, liver and brain. Data collection included clinical record review and family interview using standardized verbal autopsy. The full set of data was reviewed by local experts using a standardized process (Determination of Cause of Death) to identify all relevant conditions leading to death (causal chain), per WHO recommendations. For analysis we stratified neonatal death into 24-hours of birth, early (1-<7 days) and late (7-<28 days) neonatal deaths. We analyzed 1458 deaths, 41% occurring within 24-hours, 41% early and 18% late neonatal deaths. Leading underlying causes of death were complications of intrapartum events (31%), complications of prematurity (28%), infections (17%), respiratory disorders (11%), and congenital malformations (8%). In addition to the underlying cause, 62% of deaths had additional conditions and 14% had ≥3 other conditions in the causal chain. The most common causes considering the whole causal chain were infection (40%), prematurity (32%) and respiratory distress syndrome (28%). Common maternal conditions linked to neonatal death were maternal hypertension (10%), labour and delivery complications (8%), multiple gestation (7%), placental complications (6%) obstructed labour and chorioamnionitis (5%, each). CHAMPS’ findings showing the full causal chain of events that lead to death, in addition to maternal factors, highlights the complexities involved in each death along with the multiple opportunities for prevention. Highlighting improvements to prenatal and obstetric care and infection prevention are urgently needed in high-mortality settings.


Introduction
The child is highly vulnerable during the neonatal period. In 2019, 2.4 million children globally died in the first month of life, equivalent to 6,700 deaths per day [1]. Of those, about a third of all neonatal deaths occurred within the first day of life, and close to three-quarters occurred within the first week of life [1].
While neonatal death rates have dropped by 52% globally (from 38 to 17 deaths per 1000 live births between 1990-2019), neonatal deaths still comprise 45% of all child deaths under 5 year of age [2]. Marked disparities in neonatal mortality exist between countries and regions. Sub-Saharan Africa (SSA) and South Asia had the highest neonatal mortality, 27 and 25 deaths per 1000 live-births, respectively, in 2019 [1,3]. A child born in SSA or South Asia was 10 times more likely to die in the first month of life than a child born in a high-income country [1,4].
Sustainable Development Goal (SDG) 3.2 aims to "end all preventable deaths under 5 years of age" by 2030, with all countries aiming to reduce neonatal mortality to less than 12 deaths per 1000 live births and under-5 deaths to less than 25 deaths per 1000 live births [5]. More specific cause of death (CoD) information could help target prevention measures and achieve these targets. Currently, causes of neonatal deaths in low-and-middle-income countries are mainly inferred from vital registration and limited verbal autopsy data [6]. In 2015, only 3% of under-5 childhood cause-specific mortality fractions (CSMF) were based on adequate vital registration data, primarily from high-income countries [7]. Also, CSMF are usually derived considering only the underlying medical condition that led to death; examining the entire chain of events leading to death, including immediate and antecedent medical events, might identify more opportunities for targeted interventions and thus for preventing deaths.
The gold standard for obtaining accurate causes of death information is a complete diagnostic autopsy, more often, the procedure is not even suggested as it is not typically feasible in LMICs because of the expense, required expertise and, in some settings many families decline the procedure for personal, socio-cultural, and religious reasons [8][9][10][11]. During the past decade, use of post-mortem specimens collected through minimally invasive tissue sampling (MITS) has shed light on the sequence of events leading to deaths in children [12,13]. MITS allows post-mortem examination of critical tissues using histopathology, microbial culture, molecular detection, and other diagnostic testing such as serology and rapid tests [14].
The Child Health and Mortality Prevention Surveillance (CHAMPS) network's mission is to generate scientific knowledge to save children's lives by collecting, analyzing, and sharing accurate, timely data about the causes of child mortality in the regions where it is highest. In this manuscript, we describe conditions in the causal chain that led to neonatal deaths in our sites, including assessments of conditions for both newborns and their mothers. In addition, we evaluate whether such deaths were from preventable causes and, if so, how they might be addressed.

Methods
The analysis included deaths enrolled in CHAMPS sites who had MITS collected and whose death occurred between December 2016 and December 2021. CHAMPS protocol and methods are described elsewhere (www.champshealth.org) [12,15]. Briefly, enrollment occurred in seven countries: Bangladesh, Ethiopia, Kenya, Mali, Mozambique, Sierra Leone; and, South Africa [15].
Stillbirths and children under five years that were residing in catchment areas at the time of death were eligible for CHAMPS enrollment [16]. Parents or guardians were approached for written consent for the CHAMPS teams to conduct a standard verbal autopsy and clinical chart abstraction; for deaths identified within 24 hours (or 72 hours if refrigerated), consent was also sought for the MITS procedure. If parent were minor assent were approached from the parents and consent were approached from parent's guardians. The MITS procedure included collection of tissue from liver, lungs, and brain (through posterior and transnasal approaches) and collection of peripheral blood, cerebrospinal fluid (CSF), stool, and oropharyngeal/nasopharyngeal (OP/NP) swabs [14]. Site laboratories tested post-mortem blood samples for Human Immunodeficiency Virus DNA or RNA using polymerase chain reaction (PCR), Tuberculosis using GeneXpert and malaria using thick and thin smears and rapid diagnostic assays. Blood and CSF underwent microbial culture. PCR for screening of up to 116 pathogens was performed at each site using four custom-designed syndromic TaqMan array cards (TAC; ThermoFisher Scientific, Waltham, MA, USA) [17]. Tissue specimens were examined locally using routine histopathological techniques and, if indicated by histopathological examination or TAC results, further diagnostic tests such as special stains, immunohistochemistry, and molecular testing targeting specific microorganisms were performed at the CHAMPS Central Pathology Laboratory at the US Centers for Disease Control and Prevention (CDC) Infectious Diseases Pathology Branch [18].
DeCoDe panels convened at each site and reviewed all post-mortem diagnostic test results, pathology findings, clinical abstraction information from child and maternal health records and VA responses [15,19] for each death before assigning causes of death, taking into account all information, and using standard case definitions that include levels of diagnostic certainty [19] (available at https://champshealth.org/wp-content/uploads/2021/01/CHAMPS-Diagnosis-Standards.pdf). Level 1 was the most certain level, requiring the most evidence, and Level 3 the least certain. Panels determined each CoD and provided a causal chain [15,19], shedding light on the sequence of events that led to the fatal outcome, using WHO ICD-10 and WHO application of ICD-10 for perinatal deaths (ICD-PM) guidelines [20,21]. Panels included a diagnosis as a cause of death if the child may have survived if the condition had not occurred. For deaths in neonates attributed to a single condition, that condition was considered the underlying CoD. For deaths in which more than one condition played a role, underlying, antecedent, and immediate causes were assigned. The underlying cause occurred before immediate or comorbid conditions and may have predisposed the child to an immediate cause or co-morbid illnesses that then led to death; the immediate cause was closest to the death and the comorbid causes were in-between the underlying and immediate causes. We defined the causal chain to include all conditions listed as underlying, antecedent, and immediate causes of death. For neonatal deaths, the main maternal condition that contributed to the main or underlying condition in the neonate was also documented. For each death, the DeCoDe panel through expert consensus determined whether the death was preventable in the local context by considering the clinical, pathological, microbiological, and verbal autopsy information. The definition of preventability captures the conditions immediately surrounding the death of that particular child and not the broader political, financial, and societal influences. If the death was deemed preventable, the panel recommended health system improvements that could have prevented the death [22].
Ethics committees overseeing investigators at each site and at Emory University approved overall and site-specific protocols (Emory IRB#: 00091706). Protocols are available at: https:// champshealth.org/resources/protocols. Data analyses examined neonatal deaths for which CoD determinations were completed by a DeCoDe panel. Cases were stratified by age; death in the first 24-hours of life, early neonatal death (24-hours -<7 days; END), and late neonatal death (7-27 days; LND). Descriptive statistics and comparative chi-squared or fisher exact where appropriate were performed using Stata software version 16 (StataCorp, College Station, Texas).

Underlying causes of death
The DeCoDe panel assigned an underlying cause for all except 21 (1%) deaths in which a CoD could not be determined (Table 2). Overall, 11 different WHO ICD-PM categories were assigned for the underlying cause of the death (  Table).

Number and types of antecedent and immediate causes of death
DeCoDe panels determined that at least one other (antecedent/immediate) neonatal condition was responsible in addition to the underlying cause for 62% of deaths; 14% had 3 or more other conditions in the causal chain (Table 4). When the underlying cause was LBW/prematurity, 95% of neonatal deaths had at least one antecedent/immediate condition in addition to the underlying cause in the causal chain, and 33% had 3 or more other conditions. When the underlying cause of the death was infection, 53% of deaths had at least one other cause of the death. In contrast, for neonates with complications of an intrapartum event as the underlying  Among neonatal deaths attributed to congenital malformation as the underlying cause of the death, neonatal sepsis and lower respiratory infection were the most common immediate and antecedent conditions in the causal chain, 30% (35/118) and 21% (25/118), respectively. Among deaths in the first 24-hours of life who had congenital abnormality as the underlying Table 3 Table). When complications of an intrapartum event were the underlying cause of the death, the most common immediate and antecedent condition was neonatal encephalopathy (56/446, 13%), which was more predominant among END (39/176, 22%) than in the other age groups who had complication of intrapartum event as underlying cause of the death (Fig 4, S9 Table).  Table]). When respiratory disorder was the underlying cause of the death, neonatal sepsis was most common immediate and antecedent condition (32/159 [20%] ; Fig 6, S9 Table). Among deaths attributed to LBW/prematurity complications as the underlying cause, neonatal preterm birth complications were the most  Fig 3), complication of intrapartum event (N4, Fig 4), infection (N6, Fig 5), respiratory and cardiovascular disorder (N7, Fig 6), and low birth weight and prematurity (N9, Fig  7). There may be multiple immediate and antecedent causes of death for any individual, so the total number of causes may be greater than is listed in the figure titles.

Discussion
Our investigation of causes of death from 1458 neonates in high child mortality settings found that 5 main groups of causes (LBW, complications of intrapartum events, infections, congenital malformations, and respiratory disorders) accounted for 95% of underlying causes of death in this age group. Similar to CHAMPS findings, WHO figures state that 75% of neonatal deaths occur in the first-week of life (82% in CHAMPS), and preterm births, perinatal asphyxia, infections, and congenital defects are recognized as being the leading causes of neonatal deaths [1,2]. Likewise, modeling by IHME estimates that preterm birth, encephalopathy due to birth asphyxia and trauma, and sepsis and other infections caused about three-fourths of disability adjusted life years lost among neonatal deaths in 2019 [23] and in recent publication it has been mentioned that birth asphyxia is under rated in LMICs [24]. CHAMPS methods add to existing reports by showing the full causal chain of events in newborns that lead to death, in addition to maternal factors, providing a clearer picture of the complexities involved in these deaths than studies or estimates that apply a single, underlying cause. Among those newborns who survive their first 24-hours, a large majority had more than one condition in the casual chain leading to death, which implies more opportunities and complexities to prevent such deaths [25]. In addition, we found that the most prevalent underlying causes of

PLOS GLOBAL PUBLIC HEALTH
death shifted with the timing of the death; intrapartum events caused 42% of deaths in the first day of life but only 7% of neonatal deaths after the first week of life. Among those neonates who survived their first week but who died before reaching a month of life, most were LBW/ preterm and many succumbed to infections that may have been linked to their hospital stays.
The young median age at death (2 days) among those who underwent MITS shows the disproportionate risk in the period immediately after birth, as has been reported in previous PLOS GLOBAL PUBLIC HEALTH studies [26,27]. During the first 24-hours of life, intrapartum complications that might have been preventable with better fetal monitoring and prompt intervention-such as birth asphyxia [26,28,29] and intrauterine hypoxia [30]-caused 42% of deaths [4]. Most newborns whose deaths were attributed to intrapartum complications had no other cause of death identified and most were normal birth weight; in other words, these babies would have been healthy  Fig 9) and recommended improvements that could prevent such deaths (Fig 10).
https://doi.org/10.1371/journal.pgph.0001612.g009 babies if not for delivery complications. Three of four neonatal deaths occurring during the first 24-hours of life had a maternal condition noted, similar to findings from a study in Jordan [25] and further highlighting opportunities for identifying conditions that, had they been addressed, could have prevented deaths. Better delivery and availability of prenatal, intrapartum, and early post-partum care could prevent most of these deaths in the first day of life [22,31]. Newborns who were determined to have multiple conditions in the causal pathway leading to death commonly had neonatal encephalopathy, a condition linked to delivery complications [32], among their causes of death.
Infections played an important role in the neonatal deaths that we examined in preterm/ LBW newborns [33]. Group B Streptococcus and E. coli are known to be important causes of sepsis in the first days of life, and those pathogens were most common among deaths in the first 24-hours of life, consistent with in utero infection through vertical transmission. Our findings differ in some ways from those in the 3-country Aetiology of Neonatal Infections in South Asia (ANISA) study, which focused on community-acquired infections, used modelling to attribute causes of sepsis, and largely included newborns who survived their illnesses. In ANISA, neonatal sepsis was more often attributed to RSV and Ureaplasma, but they also found K. pneumoniae, E. coli, and other pathogens noted by CHAMPS. The CHAMPS study used much broader diagnostics and focused on neonates who died, resulting in a far higher proportion of subjects with identified infection by recognized sepsis pathogens. Gram-negative pathogens that are often resistant to first line antibiotics such as K. pneumoniae and A. baumannii were most common overall in CHAMPS and particularly among deaths after the first 24-hours. Most newborns who died from K. pneumoniae and A. baumannii likely acquired their infections after birth from the healthcare setting, given their prevalence among LNDs. Nearly 80% of A. baumannii infections were identified in the South Africa site and were mainly hospital-acquired infections. However, some of these infections caused deaths in the early neonatal period. The ANISA study also identified community-acquired, early onset infections attributed to K. pneumoniae and A. baumannii, suggesting the route of acquisition may not always be through a healthcare setting [34]. Preventing neonatal deaths through better infection prevention and control will be a challenge in facilities in LMICs as they gain greater capacity to provide supportive care to LBW newborns [33,35]. In addition to improved clinical management and quality of care, healthcare systems in LMIC will need to address the lack of equipment and reduce the number of patients each provider must manage to improve survival of LBW newborns [22].
CHAMPS' methods enable a better understanding of events that led to newborn deaths in high mortality areas, with causes of deaths confirmed by MITS [12]. Nonetheless, our methods do have some limitations. First, our surveillance teams are required to identify deaths within 24-hours (72-hours if refrigerated) so that MITS can be collected before burial or tissues start to degrade, 66 neonatal deaths that were not approached at all (shown in Fig 1), 28 (42%) were deaths in the first 24 hours, 28 (42%) were END, and 10 (15%) were LND. Such requirements mean that the deaths that are easiest to enroll, such as those that occur in health facilities, were overrepresented compared to deaths occurring in the community. This creates a bias by including only the deaths which could have a MITS completed and limits the generalizability, however the cause of death for MITS vs non-MITS is quite comparable (S3 Fig). Second, our study included broad health system improvement categories as recommendations for preventing deaths (e.g., improved clinical management and quality of care). The categories were developed from recommendations from the first DeCoDe panels and are being refined to be more specific. "Lastly, diversity among our study populations make our aggregate data more generalizable to high-mortality settings as a whole, although population characteristics might be different in each site. In particular, the main hospital in South Africa had more resources than facilities in other site, resulting in longer stays for low birth-weight newborns and more opportunity for exposure to hospital pathogens. In addition, each site's catchment areas might not be the exact representative of the whole country." How and whether the distribution of causes differs based on the location of death is unclear, although delivery complications might be more common among home deliveries and low and very LBW newborns are unlikely to survive if not brought to a healthcare setting [36]. Next, data on gestational age were not available for all deaths in our dataset; even when available the information may be inaccurate, as many pregnancies in CHAMPS sites are not evaluated with early ultrasound or other reliable dating methods. Designing interventions to prevent neonatal deaths will require more thorough examination of the specific challenges observed in each setting.
Our findings highlight the complexities and remaining opportunities for prevention of neonatal deaths. WHO through the World Health Assembly has sought commitment from countries to implement a global strategy for women's, children's and adolescent's health, including an updated report on progress in 2021 [37]. The WHO/UNICEF Every Newborn Action Plan has four components designed to end all preventable stillbirths and neonatal deaths by 2030: 1) at least four prenatal care visits for pregnant women, 2) births attended by skilled health personnel, 3) early routine postnatal care, and 4) functional level 2 inpatient units for small and ill newborns [38]. Better implementation of these components may have prevented most of the deaths we identified, as most neonatal deaths were related to pregnancy or childbirth complications and occurred in the first 2 days of life, and many had documented maternal conditions contributing to death. As most of the neonatal deaths we enrolled occurred in health facilities, health personnel should have been available; whether personnel lacked equipment they needed or require more training are questions that need more investigation. Our findings also highlight the need for better infection prevention and control for low-birth-weight newborns as more level 1 and level 2 inpatient units become available.